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Viewing changes to include/OpenMS/FORMAT/XMassFile.h

  • Committer: Package Import Robot
  • Author(s): Filippo Rusconi
  • Date: 2012-11-12 15:58:12 UTC
  • Revision ID: package-import@ubuntu.com-20121112155812-vr15wtg9b50cuesg
Tags: upstream-1.9.0
Import upstream version 1.9.0

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include/OpenMS/FORMAT/XMassFile.h
 
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// -*- mode: C++; tab-width: 2; -*-
 
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// vi: set ts=2:
 
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//
 
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// --------------------------------------------------------------------------
 
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//                    Flex series file support
 
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// --------------------------------------------------------------------------
 
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//  Copyright (C) 2009 -- Guillaume Belz (guillaume.belz@chu-lyon.fr)
 
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//
 
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//  This library is free software; you can redistribute it and/or
 
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//  modify it under the terms of the GNU Lesser General Public
 
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//  License as published by the Free Software Foundation; either
 
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//  version 2.1 of the License, or (at your option) any later version.
 
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//
 
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//  This library is distributed in the hope that it will be useful,
 
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//  but WITHOUT ANY WARRANTY; without even the implied warranty of
 
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//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 
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//  Lesser General Public License for more details.
 
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//
 
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//  You should have received a copy of the GNU Lesser General Public
 
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//  License along with this library; if not, write to the Free Software
 
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//  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
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//
 
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// --------------------------------------------------------------------------
 
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// $Maintainer: Guillaume Belz$
 
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// $Authors: Guillaume Belz$
 
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// --------------------------------------------------------------------------
 
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#ifndef OPENMS_FORMAT_XMASSFILE_H
 
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#define OPENMS_FORMAT_XMASSFILE_H
 
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#include <OpenMS/FORMAT/HANDLERS/AcqusHandler.h>
 
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#include <OpenMS/FORMAT/HANDLERS/FidHandler.h>
 
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#include <OpenMS/CONCEPT/ProgressLogger.h>
 
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#include <OpenMS/KERNEL/MSExperiment.h>
 
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namespace OpenMS
 
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{
 
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        /**
 
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                @brief File adapter for 'XMass Analysis (fid)' files.
 
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                XMass Analysis files is native format for Bruker spectrometer Flex Series.<br />
 
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                Each spectrum are saved in one directory. Each directory contains several files. 
 
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                We use 2 files for import in OpenMS :<br />
 
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                <b>acqus</b> : contains meta data about calibration (conversion for time to mz ratio), 
 
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                instrument specification and acquisition method.<br />
 
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                <b>fid</b> : contains intensity array. Intensity for each point are coded in 4 bytes integer.
 
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                @note MZ ratio are calculed with forumla based on article :<br />
 
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    <i>A database application for pre-processing, storage and comparison of mass spectra 
 
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    derived from patients and controls</i><br />
 
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    <b>Mark K Titulaer, Ivar Siccama, Lennard J Dekker, Angelique LCT van Rijswijk, 
 
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    Ron MA Heeren, Peter A Sillevis Smitt, and Theo M Luider</b><br />
 
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    BMC Bioinformatics. 2006; 7: 403<br />
 
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    http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1594579&blobtype=pdf<br />
 
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        @ingroup FileIO
 
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  */
 
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  class OPENMS_DLLAPI XMassFile
 
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          :     public ProgressLogger
 
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  {
 
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    public:
 
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      /// Default constructor
 
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      XMassFile();
 
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      /// Destructor
 
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      virtual ~XMassFile();
 
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                        /**
 
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                                @brief Loads a spectrum from a XMass file.
 
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        @param filename Name of the XMass file which should be loaded.
 
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        @param spectrum Spectrum in which the data loaded from the file should be stored.
 
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                                @exception Exception::FileNotFound is thrown if the file could not be read
 
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                        */      
 
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      template <class PeakType>
 
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      void load(const String& filename, MSSpectrum<PeakType>& spectrum)
 
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      {
 
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        Internal::AcqusHandler acqus(filename.prefix(filename.length()-3) + String("acqus"));
 
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        Internal::FidHandler fid(filename);
 
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        if (!fid)
 
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                                {
 
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                                        throw Exception::FileNotFound(__FILE__, __LINE__, __PRETTY_FUNCTION__, filename);
 
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                                }      
 
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        //  Delete old spectrum
 
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                                spectrum.clear(true);
 
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                                //temporary variables
 
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                                PeakType p;
 
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        while (spectrum.size() < acqus.getSize())
 
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        {
 
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                                  //fill peak
 
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                                  p.setPosition( (typename PeakType::PositionType) acqus.getPosition(fid.getIndex()) );
 
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                                  p.setIntensity( (typename PeakType::IntensityType) fid.getIntensity() );
 
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                                  spectrum.push_back(p);
 
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        }
 
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        fid.close();
 
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        // import metadata
 
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        spectrum.setRT(0.0);
 
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        spectrum.setMSLevel(1);
 
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        spectrum.setName("Xmass analysis file " + acqus.getParam("$ID_raw"));
 
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        spectrum.setType(SpectrumSettings::RAWDATA);
 
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        spectrum.setNativeID("spectrum=xsd:" + acqus.getParam("$ID_raw").remove('<').remove('>'));
 
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        spectrum.setComment("no comment");
 
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        InstrumentSettings instrument_settings;
 
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        instrument_settings.setScanMode(InstrumentSettings::MASSSPECTRUM);
 
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        instrument_settings.setZoomScan(false);
 
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        if(acqus.getParam(".IONIZATION MODE") == "LD+")
 
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                                {
 
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          instrument_settings.setPolarity(IonSource::POSITIVE);
 
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                                }
 
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        else if (acqus.getParam(".IONIZATION MODE") == "LD-")
 
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                                {
 
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                instrument_settings.setPolarity(IonSource::NEGATIVE);
 
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                                }
 
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        else 
 
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                                {
 
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                                        instrument_settings.setPolarity(IonSource::POLNULL);
 
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                                }
 
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        spectrum.setInstrumentSettings(instrument_settings);
 
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        AcquisitionInfo acquisition_info;
 
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        acquisition_info.setMethodOfCombination("Sum of " + acqus.getParam("$NoSHOTS") + " raw spectrum");
 
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        spectrum.setAcquisitionInfo(acquisition_info);
 
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        SourceFile source_file;
 
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        source_file.setNameOfFile("fid");
 
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        source_file.setPathToFile(filename.prefix(filename.length()-3));
 
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        source_file.setFileSize(4.0 * acqus.getSize() / 1024 / 1024); // 4 bytes / point
 
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        source_file.setFileType("Xmass analysis file (fid)");
 
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        spectrum.setSourceFile(source_file);
 
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        DataProcessing data_processing;
 
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        Software software;
 
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        software.setName("FlexControl");
 
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        String fc_ver = acqus.getParam("$FCVer"); // FlexControlVersion
 
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        if(fc_ver.hasPrefix("<flexControl "))
 
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                                {
 
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                                        fc_ver = fc_ver.suffix(' ');
 
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                                }
 
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        if(fc_ver.hasSuffix(">"))
 
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                                {
 
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                                        fc_ver = fc_ver.prefix('>');
 
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                                }
 
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        software.setVersion(fc_ver);
 
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        software.setMetaValue("Acquisition method", DataValue(acqus.getParam("$ACQMETH").remove('<').remove('>')));
 
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        data_processing.setSoftware(software);
 
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        std::set<DataProcessing::ProcessingAction> actions;
 
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        actions.insert(DataProcessing::SMOOTHING);
 
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        actions.insert(DataProcessing::BASELINE_REDUCTION);
 
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        actions.insert(DataProcessing::CALIBRATION);
 
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        data_processing.setProcessingActions(actions);
 
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        data_processing.setCompletionTime(DateTime::now());
 
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        std::vector<DataProcessing> data_processing_vector;
 
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          data_processing_vector.push_back(data_processing);
 
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        spectrum.setDataProcessing(data_processing_vector);
 
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      }
 
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                        /**
 
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                                @brief Import settings from a XMass file.
 
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        @param filename File from which the experimental settings should be loaded.
 
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        @param exp MSExperiment where the experimental settings will be stored.
 
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        @exception Exception::FileNotFound is thrown if the file could not be opened.
 
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                        */              
 
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      template <class PeakType>
 
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      void importExperimentalSettings(const String& filename, MSExperiment<PeakType>& exp)
 
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      {
 
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        Internal::AcqusHandler acqus(filename.prefix(filename.length()-3) + String("acqus"));
 
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        ExperimentalSettings& experimental_settings = exp.getExperimentalSettings();
 
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        Instrument& instrument = experimental_settings.getInstrument();
 
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        instrument.setName(acqus.getParam("SPECTROMETER/DATASYSTEM"));
 
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        instrument.setVendor(acqus.getParam("ORIGIN"));
 
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        instrument.setModel(acqus.getParam("$InstrID").remove('<').remove('>'));
 
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        std::vector<IonSource>& ionSourceList = instrument.getIonSources();
 
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        ionSourceList.clear();
 
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        ionSourceList.resize(1);
 
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        if (acqus.getParam(".INLET") == "DIRECT")
 
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                                {
 
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                ionSourceList[0].setInletType(IonSource::DIRECT);
 
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                                }
 
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        else
 
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                                {
 
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                ionSourceList[0].setInletType(IonSource::INLETNULL);
 
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          ionSourceList[0].setIonizationMethod(IonSource::MALDI);
 
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                                }
 
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        if (acqus.getParam(".IONIZATION MODE") == "LD+")
 
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                                {
 
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                ionSourceList[0].setPolarity(IonSource::POSITIVE);
 
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                                }
 
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        else if (acqus.getParam(".IONIZATION MODE") == "LD-")
 
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                                {
 
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                ionSourceList[0].setPolarity(IonSource::NEGATIVE);
 
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                                }
 
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        else 
 
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                                {
 
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                ionSourceList[0].setPolarity(IonSource::POLNULL);
 
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                                }
 
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        ionSourceList[0].setMetaValue("MALDI target reference", DataValue(acqus.getParam("$TgIDS").remove('<').remove('>')));
 
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        ionSourceList[0].setOrder(0);
 
212
            
 
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        std::vector<MassAnalyzer>& massAnalyzerList = instrument.getMassAnalyzers();
 
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        massAnalyzerList.clear();
 
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        massAnalyzerList.resize(1);  
 
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        if(acqus.getParam(".SPECTROMETER TYPE") == "TOF")
 
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                                {
 
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                massAnalyzerList[0].setType(MassAnalyzer::TOF);
 
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                                }
 
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        else
 
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                                {
 
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                massAnalyzerList[0].setType(MassAnalyzer::ANALYZERNULL);
 
223
                                }
 
224
        
 
225
        DateTime date;
 
226
        date.set(acqus.getParam("$AQ_DATE").remove('<').remove('>') );
 
227
        experimental_settings.setDateTime(date);
 
228
      }
 
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                        /**
 
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                                @brief Stores a spectrum in a XMass file (not avaible)
 
232
 
 
233
                                @exception Exception::FileNotWritable is thrown
 
234
                        */
 
235
      template <typename SpectrumType>
 
236
      void store(const String& /*filename*/, const SpectrumType& /*spectrum*/)
 
237
      {
 
238
        throw Exception::NotImplemented(__FILE__, __LINE__, __PRETTY_FUNCTION__);
 
239
      }
 
240
      
 
241
  };
 
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} // namespace OpenMS
 
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#endif // OPENMS_FORMAT_XMASSFILE_H
 
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